Genetic and genomic resources for Rubus breeding: a roadmap for the future

Extraction, purification, structural characteristics and biological properties of the polysaccharides from Rubus L: A review

Rubus L. is widely distributed throughout the world as a medicinal and food plant with rich values. There is increasing evidence that Rubus L. polysaccharides are important and representative active macromolecules with abundant in vitro and in vivo bioactivities, such as: antioxidant, immunomodulatory, hypoglycemic, anti-inflammatory, anti-tumor, anti-fatigue and so on. Despite significant advancements in research, a comprehensive and systematic review of Rubus L. polysaccharides has been absent. In this paper, we innovatively provide an in-depth overview of the extraction and purification methods, structural characterization, biological activities, possible molecular mechanisms, toxicity and applications of Rubus L. polysaccharides for the first time. In addition, the existing literature was quantitatively analyzed by bibliometrics. The paper also focuses on the challenges and future perspectives of the existing studies with a view to providing new insights and directions for the future development of Rubus L. polysaccharides.

A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry (Rubus L. subgenus Rubus Watson)

Blackberries (Rubus spp.) are globally consumed and well known for their rich anthocyanin and antioxidant content and distinct flavors. Improving blackberries has been challenging due to genetic complexity of traits and limited genomic resources. The blackberry genome has been particularly challenging to assemble due to its polyploid nature. Here, we present the first chromosome-scale and haplotype-phased assembly for the primocane-fruiting, thornless tetraploid blackberry selection BL1 (Rubus L. subgenus Rubus Watson). The genome assembly was generated using Oxford Nanopore Technology and Hi-C scaffolding, resulting in a 919 Mb genome distributed across 27 pseudochromosomes, with an N50 of 35.73 Mb. This assembly covers >92% of the genome length and contains over 98% of complete BUSCOs. Approximately, 58% of the assembly consists of repetitive sequences, with long terminal repeats being the most abundant class. A total of 87,968 protein-coding genes were predicted, of which, 82% were functionally annotated. Genome mining and RNA-Seq analyses identified possible candidate genes and transcription factors related to thornlessness and the key structural genes and transcription factors for anthocyanin biosynthesis. Activator genes including PAP1 and TTG1 and repressor genes such as ANL2 and MYBPA1 play an important role in the fine tuning of anthocyanin production during blackberry development. Resequencing of seven tetraploid blackberry cultivars/selections with different horticultural characteristics revealed candidate genes that could impact fruiting habit and disease resistance/susceptibility. This tetraploid reference genome should provide a valuable resource for accelerating genetic analysis of blackberries and facilitating the development of new improved cultivars with enhanced horticultural and nutritional traits.

Genetic Diversity Assessment and Core Germplasm Screening of Blackcurrant (Ribes nigrum) in China via Expressed Sequence Tag-Simple Sequence Repeat Markers

Blackcurrant (Ribes nigrum L.) has high nutritional value for human health due to its abundant vitamin C, flavonoids, and organic acids. However, its breeding and genetic research have been severely hindered by the lack of scientific tools such as molecular markers. Here, we identified 14,258 EST-SSR loci from 9531 CDS sequences with lengths greater than 1 kb, which comprised 6211 mononucleotide repeats, 4277 dinucleotide repeats, and 2469 trinucleotide repeats. We then randomly selected 228 EST-SSR loci for PCR amplification and gel electrophoresis imaging in the Ribes collection of Northeast Agricultural University (95 blackcurrant cultivars and 12 other Ribes accessions). As a result, 31 pairs of markers produced clear and reproducible bands of the expected size. Based on the 107 Ribes accessions, the allele number (Na), information index (I), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphic information content (PIC) of the 31 markers were 2-5, 0.23-1.32, 0.07-0.71, 0.11-0.68, and 0.14-0.67, respectively. For the blackcurrant gene pool, neighbor-joining and population structure analysis revealed three clusters, which did not align well with their geographical origins. Based on the results, two sets with 21 and 19 blackcurrant cultivars were identified by Power Core (PC) and Core Hunter (CH) programs. The integrated core germplasm (IC) set with 27 cultivars derived from the PC and CH sets harbored abundant genetic diversity, where the allele retention rate accounted for 98.9% of the blackcurrant gene pool. The SSR markers, data, and core germplasms presented in this study lay a solid foundation for the phylogenetic study, molecular breeding, and conservation genetics of Ribes, especially Ribes nigrum.

Evaluating shoot-tip regrowth of 25 Rubus L. species and hybrids after 15 to 20 years of cryopreserved storage

Rubus L. species are pan-global in their distribution and used as food throughout the world. Their fruits, collectively called brambles, come in a variety of colors from black, through various shades of red and yellow to white. The USDA-ARS, National Plant Germplasm System maintains >2250 accession seed- and screenhouse-based Rubus collection in Corvallis, OR and the USDA-ARS, National Laboratory for Genetic Resources Preservation in Fort Collins, CO has cryopreserved and maintains 200 accessions in liquid nitrogen (LN). We investigated regrowth of 25 selected Rubus accessions cryopreserved by droplet vitrification and stored cryogenically for 15-20 years, to determine the need for possible repropagation and reprocessing. The initial regrowth of the stored accessions after 24 h in LN ranged from 50 to 100 %. After long-term LN storage, overall regrowth was significantly lower than the initial regrowth (on the average for the 25 accessions by 8.7 %). However, except for one accession with recovery of 23 % (R. laciniatus PI 553651), the regrowth of the other 24 accessions ranged from 40 to 100 %, with 16 accessions at >73 % regrowth. High initial viability was important for recovering large numbers of living shoots after long-term storage. Extending regrowth of five accessions from six to 12 wk did not significantly increase the regrowth, suggesting that a 6-wk cultivation is sufficient for regrowth assessment. Knowledge of changes in viability over time in cryopreserved collections is vital information for curators to determine what repropagation intervals are needed for specific germplasm collections. These studies also provide large-scale information on changes that might be needed in the cryopreservation protocol for the next storage cycle.

Characteristics and phylogenetic analysis of the complete chloroplast genome of Rubus swinhoei Hance 1866 from the family Rosaceae

Rubus swinhoei Hance is an important plant owing to its medicinal root and edible fruit, and extensively distributed in China. In this study, we reported the complete chloroplast genome of R. swinhoei. The chloroplast genome was 156,335 bp in size with the overall GC content of 37.15%, having a circular and quadripartite structure, which contained a large single-copy (LSC) and a small single-copy (SSC) regions of 85,897 bp and 18,858 bp separated by a pair of 25,790 bp inverted repeat (IR) regions. The complete chloroplast genome comprised 131 unique genes of which 86 and 37 were protein-coding genes and tRNA genes, respectively, and also eight rRNA genes. The phylogenetic analysis revealed that R. swinhoei was closely related to R. kawakamii. The genome information reported in this paper will be beneficial for further investigation on the evolution of this species.

Prediction of the potential distribution of a raspberry (Rubus idaeus) in China based on MaxEnt model

Rubus idaeus is a pivotal cultivated species of raspberry known for its attractive color, distinct flavor, and numerous health benefits. It can be used in pharmaceutical, cosmetics, agriculture and food industries not only as fresh but also as a processed product. Nowadays due to climatic changes, genetic diversity of cultivars has decreased dramatically. However, until now, the status of wild R. idaeus resources in China have not been exploited. In this study, we investigated the resources of wild R. idaeus in China to secure its future potential and sustainability. The MaxEnt model was used to predict R. idaeus suitable habitats and spatial distribution patterns for current and future climate scenarios, based on wild domestic geographic distribution data, current and future climate variables, and topographic variables. The results showed that, mean temperature of the coldest quarter (bio11), precipitation of the coldest quarter (bio19), precipitation of the warmest quarter (bio18), and temperature seasonality (bio4) were crucial factors affecting the distribution of R. idaeus. Presently, the suitable habitats were mainly distributed in the north of China including Xinjiang, Inner Mongolia, Gansu, Ningxia, Shaanxi, Shanxi, Hebei, Beijing, Liaoning, Jilin, Heilongjiang. According to our results, in 2050s, the total suitable habitat area of R. idaeus will increase under SSP1-2.6 and then will be decreased with climate change, while in the 2090s, the total suitable habitat area will continue to decrease. From the present to the 2090s, the centroid distribution of R. idaeus in China will shift towards the east and the species will always be present in Inner Mongolia. Our results provide wild resource information and theoretical reference for the protection and rational utilization of R. idaeus.

Altered expression of a raspberry homologue of VRN1 is associated with disruption of dormancy induction and misregulation of subsets of dormancy-associated genes

Winter dormancy is a key process in the phenology of temperate perennials. Climate change is severely impacting its course leading to economic losses in agriculture. A better understanding of the underlying mechanisms, as well as the genetic basis of the different responses, is necessary for the development of climate-resilient cultivars. This study aims to provide an insight into winter dormancy in red raspberry (Rubus idaeus L). We report the transcriptomic profiles during dormancy in two raspberry cultivars with contrasting responses. The cultivar 'Glen Ample' showed a typical perennial phenology, whereas 'Glen Dee' registered consistent dormancy dysregulation, exhibiting active growth and flowering out of season. RNA-seq combined with weighted gene co-expression network analysis identified gene clusters in both genotypes that exhibited time-dependent expression profiles. Functional analysis of 'Glen Ample' gene clusters highlighted the significance of the cell and structural development prior to dormancy entry as well the role of genetic and epigenetic processes such as RNAi and DNA methylation in regulating gene expression. Dormancy release in 'Glen Ample' was associated with up-regulation of transcripts associated with the resumption of metabolism, nucleic acid biogenesis, and processing signal response pathways. Many of the processes occurring in 'Glen Ample' were dysregulated in 'Glen Dee' and 28 transcripts exhibiting time-dependent expression in 'Glen Ample' that also had an Arabidopsis homologue were not found in 'Glen Dee'. These included a gene with homology to Arabidopsis VRN1 (RiVRN1.1) that exhibited a sharp decline in expression following dormancy induction in 'Glen Ample'. Characterization of the gene region in the 'Glen Dee' genome revealed two large insertions upstream of the ATG start codon. We propose that expression below detection level of a specific VRN1 homologue in 'Glen Dee' causes dormancy misregulation as a result of inappropriate expression of a subset of genes that are directly or indirectly regulated by RiVRN1.1.

Chromosome-scale genome, together with transcriptome and metabolome, provides insights into the evolution and anthocyanin biosynthesis of Rubus rosaefolius Sm. (Rosaceae)

Rubus rosaefolius is a kind of red raspberry possessing high nutritional and pharmaceutical value. Here we present a chromosome-level draft genome of R. rosaefolius. Of the total 131 assembled scaffolds, 70 with a total size of 219.02 Mb, accounting for 99.33% of the estimated genome size, were anchored to seven pseudochromosomes. We traced a whole-genome duplication (WGD) event shared among members of the Rosaceae family, from which were derived 5090 currently detectable duplicated gene pairs (dgps). Of the WGD-dgps 75.09% underwent purifying selection, and approximately three-quarters of informative WGD-dgps expressed their two paralogs with significant differences. We detected a wide variety of anthocyanins in the berries of R. rosaefolius, and their total concentration remained relatively stable during berry development but increased rapidly during the ripening stage, mainly because of the contributions of pelargonidin-3-O-glucoside and pelargonidin-3-O-(6″-O-malonyl)glucoside. We identified many structural genes that encode enzymes, such as RrDFR, RrF3H, RrANS, and RrBZ1, and play key roles in anthocyanin biosynthesis. The expression of some of these genes significantly increased or decreased with the accumulation of pelargonidin-3-O-glucoside and pelargonidin-3-O-(6″-O-malonyl)glucoside. We also identified some transcription factors and specific methylase-encoding genes that may play a role in regulating anthocyanin biosynthesis by targeting structural genes. In conclusion, our findings provide deeper insights into the genomic evolution and molecular mechanisms underlying anthocyanin biosynthesis in berries of R. rosaefolius. This knowledge may significantly contribute to the targeted domestication and breeding of Rubus species.

Genome-Wide Identification of Expansins in Rubus chingii and Profiling Analysis during Fruit Ripening and Softening

Improving fruit size or weight, firmness, and shelf life is a major target for horticultural crop breeding. It is associated with the depolymerization and rearrangement of cell components, including pectin, hemicellulose, cellulose, and other structural (glyco)proteins. Expansins are structural proteins to loosen plant cell wall polysaccharides in a pH-dependent manner and play pivotal roles in the process of fruit development, ripening, and softening. Rubus chingii Hu, a unique Chinese red raspberry, is a prestigious pharmaceutical and nutraceutical dual-function food with great economic value. Thirty-three RchEXPs were predicted by genome-wide identification in this study, containing twenty-seven α-expansins (EXPAs), three β-expansins (EXPBs), one expansin-like A (EXPLA), and two expansin-like B (EXPLBs). Subsequently, molecular characteristics, gene structure and motif compositions, phylogenetic relationships, chromosomal location, collinearity, and regulatory elements were further profiled. Furthermore, transcriptome sequencing (RNA-seq) and real-time quantitative PCR assays of fruits from different developmental stages and lineages showed that the group of RchEXPA5, RchEXPA7, and RchEXPA15 were synergistically involved in fruit expanding and ripening, while another group of RchEXPA6 and RchEXPA26 might be essential for fruit ripening and softening. They were regulated by both abscisic acid and ethylene and were collinear with phylogenetic relationships in the same group. Our new findings laid the molecular foundation for improving the fruit texture and shelf life of R. chingii medicinal and edible fruit.

The Influence of the Explant's Type on the Performance of Synthetic Seeds of Blackberry (Rubus spp.)

In vitro propagation, also known as micropropagation, has become the most widely employed method for blackberry propagation, as it overcomes the limitations of the traditional asexual propagation methods (mainly layering and cutting). In this context, synthetic seed technology represents a strategy to enhance the productivity of in vitro propagation and facilitates the exchange of plant materials between laboratories, contributing to germplasm conservation. This study aimed to identify the most suitable vegetative propagule for the encapsulation of blackberry. To this end, uninodal microcuttings (nodes) and the base of clumps were used to produce synthetic seeds for the cultivars Thornfree and Chester. Forty-five days after sowing, viability (percentage of green propagules without browning or necrosis), regeneration (percentage of propagules that sprouted and rooted simultaneously), number of shoots produced, shoot length, number of roots produced, root length, and the fresh and dry weights of the plantlets were measured. The results demonstrated that both considered propagules allowed us to obtain satisfactory regeneration rates. However, plantlets originating from the encapsulated clump's base had more shoots and roots, resulting in greater fresh and dry weights than the plantlets derived from encapsulated nodes. Therefore, for achieving more robust plantlets and enhancing overall procedural efficiency, we recommend using the base of clumps as a propagule for blackberry encapsulation.

Untapped potential of non-conventional rubus species: bioactivity, nutrition, and livelihood opportunities

Rubus species holds promise as a valuable source of polyphenols and bioactive compounds, offering significant potential as functional food ingredients with both nutraceutical and pharmaceutical benefits. However, many edible species within this genus remain under-explored and their importance is largely unrecognized. This review aims to provide an overview of the nutritional and bioactive components of both explored and under-explored Rubus species, highlighting their potential health advantages, value addition, and recent advancements. The economic exploitation of Rubus is currently limited to a few cultivated species, while numerous non-conventional and wild edible species are overlooked. Recognizing the economic and nutritional significance of exploited Rubus species, it is imperative to explore the untapped potential of these underutilized plants. By doing so, these species can be preserved from endangerment and contribute to nutritional and livelihood security for communities having access to them. This review emphasizes the importance of understanding the exceptional characteristics of Rubus species as "superfoods" and encourages the promotion and cultivation of these unexplored species. By expanding the cultivation and utilization of under-explored Rubus species, we can unlock their full potential and support sustainable nutritional and economic benefits.

A multiplexed plant-animal SNP array for selective breeding and species conservation applications

Reliable and high-throughput genotyping platforms are of immense importance for identifying and dissecting genomic regions controlling important phenotypes, supporting selection processes in breeding programs, and managing wild populations and germplasm collections. Amongst available genotyping tools, single nucleotide polymorphism arrays have been shown to be comparatively easy to use and generate highly accurate genotypic data. Single-species arrays are the most commonly used type so far; however, some multi-species arrays have been developed for closely related species that share single nucleotide polymorphism markers, exploiting inter-species cross-amplification. In this study, the suitability of a multiplexed plant-animal single nucleotide polymorphism array, including both closely and distantly related species, was explored. The performance of the single nucleotide polymorphism array across species for diverse applications, ranging from intra-species diversity assessments to parentage analysis, was assessed. Moreover, the value of genotyping pooled DNA of distantly related species on the single nucleotide polymorphism array as a technique to further reduce costs was evaluated. Single nucleotide polymorphism performance was generally high, and species-specific single nucleotide polymorphisms proved suitable for diverse applications. The multi-species single nucleotide polymorphism array approach reported here could be transferred to other species to achieve cost savings resulting from the increased throughput when several projects use the same array, and the pooling technique adds another highly promising advancement to additionally decrease genotyping costs by half.

Construction and genetic characterization of an interspecific raspberry hybrids panel aiming resistance to late leaf rust and adaptation to tropical regions

Raspberries (Rubus spp) are temperate climate fruits with profitable high returns and have the potential for diversification of fruit growing in mid to low-latitude regions. However, there are still no cultivars adapted to climatic conditions and high pressure of diseases that occurs in tropical areas. In this context, our objective was to evaluate the genetic diversity from a 116 raspberry genotypes panel obtained from interspecific crosses in a testcross scheme with four cultivars already introduced in Brazil. The panel was genotyped via genotyping-by-sequencing. 28,373 and 27,281 SNPs were obtained, using the species R. occidentalis and R. idaeus genomes as references, respectively. A third marker dataset was constructed consisting of 41,292 non-coincident markers. Overall, there were no differences in the results when using the different marker sets for the subsequent analyses. The mean heterozygosity was 0.54. The average effective population size was 174, indicating great genetic variability. The other analyses revealed that the half-sibling families were structured in three groups. It is concluded that the studied panel has great potential for breeding and further genetic studies. Moreover, only one of the three marker matrices is sufficient for diversity studies.

Blackberries and Mulberries: Berries with Significant Health-Promoting Properties

Blackberries and mulberries are small and perishable fruits that provide significant health benefits when consumed. In reality, both are rich in phytochemicals, such as phenolics and volatile compounds, and micronutrients, such as vitamins. All the compounds are well-known thanks to their medicinal and pharmacological properties, namely antioxidant, anti-inflammatory, anti-cancer, antiviral, and cardiovascular properties. Nevertheless, variables such as genotype, production conditions, fruit ripening stage, harvesting time, post-harvest storage, and climate conditions influence their nutritional composition and economic value. Given these facts, the current review focuses on the nutritional and chemical composition, as well as the health benefits, of two blackberry species (Rubus fruticosus L., and Rubus ulmifolius Schott) and one mulberry species (Morus nigra L.).

Design, execution, and interpretation of plant RNA-seq analyses

Genomics has transformed our understanding of the genetic architecture of traits and the genetic variation present in plants. Here, we present a review of how RNA-seq can be performed to tackle research challenges addressed by plant sciences. We discuss the importance of experimental design in RNA-seq, including considerations for sampling and replication, to avoid pitfalls and wasted resources. Approaches for processing RNA-seq data include quality control and counting features, and we describe common approaches and variations. Though differential gene expression analysis is the most common analysis of RNA-seq data, we review multiple methods for assessing gene expression, including detecting allele-specific gene expression and building co-expression networks. With the production of more RNA-seq data, strategies for integrating these data into genetic mapping pipelines is of increased interest. Finally, special considerations for RNA-seq analysis and interpretation in plants are needed, due to the high genome complexity common across plants. By incorporating informed decisions throughout an RNA-seq experiment, we can increase the knowledge gained.

Genome-wide association identifies key loci controlling blackberry postharvest quality

Introduction

Blackberry (Rubus subgenus Rubus) is a soft-fruited specialty crop that often suffers economic losses due to degradation in the shipping process. During transportation, fresh-market blackberries commonly leak, decay, deform, or become discolored through a disorder known as red drupelet reversion (RDR). Over the past 50 years, breeding programs have achieved better fruit firmness and postharvest quality through traditional selection methods, but the underlying genetic variation is poorly understood.

Methods

We conducted a genome-wide association of fruit firmness and RDR measured in 300 tetraploid fresh-market blackberry genotypes from 2019-2021 with 65,995 SNPs concentrated in genic regions of the R. argutus reference genome.

Results

Fruit firmness and RDR had entry-mean broad sense heritabilities of 68% and 34%, respectively. Three variants on homologs of polygalacturonase (PG), pectin methylesterase (PME), and glucan endo-1,3-β-glucosidase explained 27% of variance in fruit firmness and were located on chromosomes Ra06, Ra01, and Ra02, respectively. Another PG homolog variant on chromosome Ra02 explained 8% of variance in RDR, but it was in strong linkage disequilibrium with 212 other RDR-associated SNPs across a 23 Mb region. A large cluster of six PME and PME inhibitor homologs was located near the fruit firmness quantitative trait locus (QTL) identified on Ra01. RDR and fruit firmness shared a significant negative correlation (r = -0.28) and overlapping QTL regions on Ra02 in this study.

Discussion

Our work demonstrates the complex nature of postharvest quality traits in blackberry, which are likely controlled by many small-effect QTLs. This study is the first large-scale effort to map the genetic control of quantitative traits in blackberry and provides a strong framework for future GWAS. Phenotypic and genotypic datasets may be used to train genomic selection models that target the improvement of postharvest quality.

Investigating Biochemical and Histopathological Responses between Raspberries and Aculeastrum americanum

Late leaf rust is a fungal disease in raspberries caused by Aculeastrum americanum (Farl.) M. Scholler U. Braun (syn. Thekopsora americana (Farl.) Aime McTaggart) leading to early defoliation and yield losses. Red raspberries (Rubus idaeus L.) are susceptible to this pathogen, although this susceptibility varies among cultivars. In contrast, black raspberries were previously reported to be more resistant (Rubus occidentalis L.) and immune (Rubus niveus Thunb.) to this pathogen, raising their importance in plant breeding programs. However, what features make them respond differently to the same pathogen? In this study, we characterize for the first time the pre- and post-formed structural and biochemical defense mechanisms of R. idaeus cv. Autumn Bliss, R. occidentalis and R. niveus. Ultrastructural and histopathological analyses were used to uncover the interactions between these raspberries and A. americanum. The ultrastructural results indicate that the pathogen germinates on both leaf surfaces but can only form appressoria on the stomata. Although the three raspberry species were infected and colonized by A. americanum, a clear difference in susceptibility was observed between them. A compact mesophyll, pre- and post-formed phenolic compounds, and post-formed pectic compounds were the main plant defense mechanisms against fungal colonization. These findings provide new information about raspberries’ defense mechanisms in response to A. americanum and elucidate the interactions occurring in these pathosystems.

Novel Approaches for Sustainable Horticultural Crop Production: Advances and Prospects

Reduction of plant growth, yield and quality due to diverse environmental constrains along with climate change significantly limit the sustainable production of horticultural crops. In this review, we highlight the prospective impacts that are positive challenges for the application of beneficial microbial endophytes, nanomaterials (NMs), exogenous phytohormones strigolactones (SLs) and new breeding techniques (CRISPR), as well as controlled environment horticulture (CEH) using artificial light in sustainable production of horticultural crops. The benefits of such applications are often evaluated by measuring their impact on the metabolic, morphological and biochemical parameters of a variety of cultures, which typically results in higher yields with efficient use of resources when applied in greenhouse or field conditions. Endophytic microbes that promote plant growth play a key role in the adapting of plants to habitat, thereby improving their yield and prolonging their protection from biotic and abiotic stresses. Focusing on quality control, we considered the effects of the applications of microbial endophytes, a novel class of phytohormones SLs, as well as NMs and CEH using artificial light on horticultural commodities. In addition, the genomic editing of plants using CRISPR, including its role in modulating gene expression/transcription factors in improving crop production and tolerance, was also reviewed.

A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.)

Rubus idaeus L. (red raspberry), is a perennial woody plant species of the Rosaceae family that is widely cultivated in the temperate regions of world and is thus an economically important soft fruit species. It is prized for its flavour and aroma, as well as a high content of healthful compounds such as vitamins and antioxidants. Breeding programs exist globally for red raspberry, but variety development is a long and challenging process. Genomic and molecular tools for red raspberry are valuable resources for breeding. Here, a chromosome-length genome sequence assembly and related gene predictions for the red raspberry cultivar 'Anitra' are presented, comprising PacBio long read sequencing scaffolded using Hi-C sequence data. The assembled genome sequence totalled 291.7 Mbp, with 247.5 Mbp (84.8%) incorporated into seven sequencing scaffolds with an average length of 35.4 Mbp. A total of 39,448 protein-coding genes were predicted, 75% of which were functionally annotated. The seven chromosome scaffolds were anchored to a previously published genetic linkage map with a high degree of synteny and comparisons to genomes of closely related species within the Rosoideae revealed chromosome-scale rearrangements that have occurred over relatively short evolutionary periods. A chromosome-level genomic sequence of R. idaeus will be a valuable resource for the knowledge of its genome structure and function in red raspberry and will be a useful and important resource for researchers and plant breeders.

Study on Supergenus Rubus L.: Edible, Medicinal, and Phylogenetic Characterization

Rubus L. is one of the most diverse genera belonging to Rosaceae; it consists of more than 700 species with a worldwide distribution. It thus provides an ideal natural "supergenus" for studying the importance of its edible, medicinal, and phylogenetic characteristics for application in our daily lives and fundamental scientific studies. The Rubus genus includes many economically important species, such as blackberry (R. fruticosus L.), red raspberry (R. ideaus L.), black raspberry (R. occidentalis L.), and raspberry (R. chingii Hu), which are widely utilized in the fresh fruit market and the medicinal industry. Although Rubus species have existed in human civilization for hundreds of years, their utilization as fruit and in medicine is still largely inadequate, and many questions on their complex phylogenetic relationships need to be answered. In this review, we briefly summarize the history and progress of studies on Rubus, including its domestication as a source of fresh fruit, its medicinal uses in pharmacology, and its systematic position in the phylogenetic tree. Recent available evidence indicates that (1) thousands of Rubus cultivars were bred via time- and labor-consuming methods from only a few wild species, and new breeding strategies and germplasms were thus limited; (2) many kinds of species in Rubus have been used as medicinal herbs, though only a few species (R. ideaus L., R. chingii Hu, and R. occidentalis L.) have been well studied; (3) the phylogeny of Rubus is very complex, with the main reason for this possibly being the existence of multiple reproductive strategies (apomixis, hybridization, and polyploidization). Our review addresses the utilization of Rubus, summarizing major relevant achievements and proposing core prospects for future application, and thus could serve as a useful roadmap for future elite cultivar breeding and scientific studies.

Phenolic profiles and their responses to pre- and post-harvest factors in small fruits: a review

The consumption of small fruits has increased in recent years. Besides their appealing flavor, the commercial success of small fruits has been partially attributed to their high contents of phenolic compounds with multiple health benefits. The phenolic profiles and contents in small fruits vary based on the genetic background, climate, growing conditions, and post-harvest handling techniques. In this review, we critically compare the profiles and contents of phenolics such as anthocyanins, flavonols, flavan-3-ols, and phenolic acids that have been reported in bilberries, blackberries, blueberries, cranberries, black and red currants, raspberries, and strawberries during fruit development and post-harvest storage. This review offers researchers and breeders a general guideline for the improvement of phenolic composition in small fruits while considering the critical factors that affect berry phenolics from cultivation to harvest and to final consumption.

Combined transcriptomic and metabolic analyses reveal potential mechanism for fruit development and quality control of Chinese raspberry (Rubus chingii Hu)

Combined transcriptomic and metabolic analyses reveal that fruit of Rubus chingii Hu launches biosynthesis of phenolic acids and flavonols at beginning of fruit set and then coordinately accumulated or converted to their derivatives. Rubus chingii Hu (Chinese raspberry) is an important dual functional food with nutraceutical and pharmaceutical values. Comprehensively understanding the mechanisms of fruit development and bioactive components synthesis and regulation could accelerate genetic analysis and molecular breeding for the unique species. Combined transcriptomic and metabolic analyses of R. chingii fruits from different developmental stages, including big green, green-to-yellow, yellow-to-orange, and red stages, were conducted. A total of 89,188 unigenes were generated and 57,545 unigenes (64.52%) were annotated. Differential expression genes (DEGs) and differentially accumulated metabolites (DAMs) were mainly involved in the biosynthesis of secondary metabolites. The fruit launched the biosynthesis of phenolic acids and flavonols at the very beginning of fruit set and then coordinately accumulated or converted to their derivatives. This was tightly regulated by expressions of the related genes and MYB and bHLH transcription factors. The core genes products participated in the biosynthesis of ellagic acid (EA) and kaempferol-3-O-rutinoside (K-3-R), such as DAHPS, DQD/SDH, PAL, 4CL, CHS, CHI, F3H, F3'H, FLS, and UGT78D2, and their corresponding metabolites were elaborately characterized. Our research reveals the molecular and chemical mechanisms of the fruit development of R. chingii. The results provide a solid foundation for the genetic analysis, functional genes isolation, fruit quality improvement and modifiable breeding of R. chingii.

Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.

High-Density Linkage Map Construction and QTL Identification in a Diploid Blueberry Mapping Population

Genotyping by sequencing approaches have been widely applied in major crops and are now being used in horticultural crops like berries and fruit trees. As the original and largest producer of cultivated blueberry, the United States maintains the most diverse blueberry germplasm resources comprised of many species of different ploidy levels. We previously constructed an interspecific mapping population of diploid blueberry by crossing the parent F₁#10 (Vaccinium darrowii Fla4B × diploid V. corymbosum W85-20) with the parent W85-23 (diploid V. corymbosum). Employing the Capture-Seq technology developed by RAPiD Genomics, with an emphasis on probes designed in predicted gene regions, 117 F₁ progeny, the two parents, and two grandparents of this population were sequenced, yielding 131.7 Gbp clean sequenced reads. A total of 160,535 single nucleotide polymorphisms (SNPs), referenced to 4,522 blueberry genome sequence scaffolds, were identified and subjected to a parent-dependent sliding window approach to further genotype the population. Recombination breakpoints were determined and marker bins were deduced to construct a high density linkage map. Twelve blueberry linkage groups (LGs) consisting of 17,486 SNP markers were obtained, spanning a total genetic distance of 1,539.4 cM. Among 18 horticultural traits phenotyped in this population, quantitative trait loci (QTLs) that were significant over at least 2 years were identified for chilling requirement, cold hardiness, and fruit quality traits of color, scar size, and firmness. Interestingly, in 1 year, a QTL associated with timing of early bloom, full bloom, petal fall, and early green fruit was identified in the same region harboring the major QTL for chilling requirement. In summary, we report here the first high density bin map of a diploid blueberry mapping population and the identification of several horticulturally important QTLs.

A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding

A Rosaceae family-level candidate gene approach was used to identify genes associated with sugar content in blackberry (Rubus subgenus Rubus). Three regions conserved among apple (Malus × domestica), peach (Prunus persica), and alpine strawberry (Fragaria vesca) were identified that contained previously detected sweetness-related quantitative trait loci (QTL) in at least two of the crops. Sugar related genes from these conserved regions and 789 sugar-associated apple genes were used to identify 279 Rubus candidate transcripts. A Hyb-Seq approach was used in conjunction with PacBio sequencing to generate haplotype level sequence information of sugar-related genes for 40 cultivars with high and low soluble solids content from the University of Arkansas and USDA blackberry breeding programs. Polymorphisms were identified relative to the ‘Hillquist’ blackberry (R. argutus) and ORUS 4115-3 black raspberry (R. occidentalis) genomes and tested for their association with soluble solids content (SSC). A total of 173 alleles were identified that were significantly (α = 0.05) associated with SSC. KASP genotyping was conducted for 92 of these alleles on a validation set of blackberries from each breeding program and 48 markers were identified that were significantly associated with SSC. One QTL, qSSC-Ruh-ch1.1, identified in both breeding programs accounted for an increase of 1.5 °Brix and the polymorphisms were detected in the intron space of a sucrose synthase gene. This discovery represents the first environmentally stable sweetness QTL identified in blackberry. The approach demonstrated in this study can be used to develop breeding tools for other crops that have not yet benefited directly from the genomics revolution.

Comparison of the Micromorphology and Ultrastructure of Pollen Grains of Selected Rubus idaeus L. Cultivars Grown in Commercial Plantation

The genus Rubus is one of the largest taxonomically diverse and complex genera in the family Rosaceae. Morphology of pollen grains (equatorial and polar axes length, shape and size, aperture position, exine sculpture, perforations) is regarded as one of its main diagnostic features for identification of species and varieties. An attempt was made to fill the gap concerning the pollen micromorphology and ultrastructure of R. idaeus L. using light, scanning, and electron transmission microscopy. This study is a comparative analysis of micromorphological and ultrastructural traits of pollen from six raspberry cultivars. The pollen grains were classified as small or medium of shape prolato-spheroids. The parallel striae in the equatorial view in the exine sculpture were sometimes branched dichotomously in ‘Glen Ample’, ‘Polka’, and ‘Polana’, arcuate in ‘Laszka’ and ‘Pokusa’, or irregularly overlapping in ‘Radziejowa’. The width of exine striae of biennial fruiting cultivars was much larger than in repeated fruiting cultivars. In terms of the increasing number of perforations per unit area of the exine surface, the cultivars were ranked as follows: ‘Pokusa’ < ‘Glen Ample’ < ‘Laszka’ < ‘Polka’ < ‘Polana’ < ‘Radziejowa’. The thickest tectum, the highest and thickest columellae with the largest distances between them, and the thicker foot layer were demonstrated in ‘Glen Ample’. The ectoexine constituted on average ca. 78–90% of the exine thickness. The findings may constitute auxiliary traits i.a. for identification of related taxa, interpretation of phylogenetic relationships, and pollination biology.

Transferability and Polymorphism of SSR Markers Located in Flavonoid Pathway Genes in Fragaria and Rubus Species

Strawberry (Fragaria) and raspberry (Rubus) are very popular crops, and improving their nutritional quality and disease resistance are important tasks in their breeding programs that are becoming increasingly based on use of functional DNA markers. We identified 118 microsatellite (simple sequence repeat-SSR) loci in the nucleotide sequences of flavonoid biosynthesis and pathogenesis-related genes and developed 24 SSR markers representing some of these structural and regulatory genes. These markers were used to assess the genetic diversity of 48 Fragaria and Rubus specimens, including wild species and rare cultivars, which differ in berry color, ploidy, and origin. We have demonstrated that a high proportion of the developed markers are transferable within and between Fragaria and Rubus genera and are polymorphic. Transferability and polymorphism of the SSR markers depended on location of their polymerase chain reaction (PCR) primer annealing sites and microsatellite loci in genes, respectively. High polymorphism of the SSR markers in regulatory flavonoid biosynthesis genes suggests their allelic variability that can be potentially associated with differences in flavonoid accumulation and composition. This set of SSR markers may be a useful molecular tool in strawberry and raspberry breeding programs for improvement anthocyanin related traits.